They probably never would have got a chance to use it.
Each plane has a 4 digit transponder code (known as squawk) assigned by air traffic control. To quietly signal you've been hijacked, you change the squawk code to 7500.
Not one of the hijacked planes squawked 7500. Either the hijackers were wise to this move and explicitly prevented it or they didn't give the pilots time to make any moves at all.
Given the capabilities of modern autopilots, its quite feasible to lock out cockpit controls and force the plane into a holding pattern remotely, but there's all kinds of other scenarios where this would be worse. For instance, radio or other failure endangers the aircraft, activates the system, and renders the pilot unable to take action to save his passengers. That would be unacceptable should such a thing happen. Besides, you could always hack it somehow using manual flight controls like rewiring the hydraulic controls.
Its like the damn liferafts over-water flights have to carry. They take up all the overhead stowage and there's never been a case of an airliner sucessfully ditching. They always are completely destroyed on impact. But as a pilot friend explained to me, if a plane ever did ditch and there were no rafts, the public outcry would be frightening - so planes carry liferafts.
